Best Intro FMV: FFVIII...hands down.

Best mid-game FMV: The one where they were sliding out of the airship from FFX...pure sweetness. Or just about all of the rest of the FFX FMVs.

Best Ending FMV: FFX...I'm a guy, and I was 17 at the time, and I sat there crying my ass off...plus it was just such a beautiful, touching piece of work by itself.